Burundi opposition leader Agathon Rwasa on Thursday took up the position of deputy speaker in parliament after an election which his coalition had boycotted, prompting a political ally to say the move could cause a split in their alliance.

The United States had called the July 21 presidential vote "deeply flawed", while regional observers said the poll "fell short" of being free and fair.

Rwasa, the leader of the opposition Amizero y'Abarundi coalition, had staunchly opposed President Pierre Nkurunziza, whose decision to seek a third term in office plunged Burundi into its biggest crises since a civil war ended in 2005.

Rwasa and lawmakers from his coalition boycotted both the presidential and parliamentary elections, saying the government had used violence to intimidate their members and curtailed free speech by shutting private media.

But since Nkurunziza's victory, the opposition has split over whether to take up their seats in the parliament. They boycotted the polls, but candidates' names were kept on the ballot papers and some of them won seats.

Charles Nditije, from the opposition Uprona party that acts as the junior partner in the Amizero y'Abarundi coalition, said the coalition could be ruptured by Rwasa, who was elected vice president of the national assembly on Thursday.

Some opposition figures fear Rwasa could join the cabinet to form a unity government with Nkurunziza without the preconditions he had previously outlined - a move they believe would fracture his party's alliance with Nditije's Uprona.

"If Rwasa [joins the cabinet] of Nkurunziza - which will not organize other credible, inclusive and democratic elections within a year - then we will separate," Nditije told Reuters, referring to opposition demands for a re-run of the presidential poll.

It is not clear if Rwasa would oppose the government from within the national assembly, or vote with the government, having been elected to a senior role.

Pascal Nyabenda, president of Nkurunziza's ruling CNDD-FDD party, has been appointed speaker.

Twenty lawmakers from Rwasa's FNL party, the senior partner in the opposition alliance, took up their seats in the parliament earlier this week. Nine members of Nditije's Uprona party have said they would not join the 121-member chamber, while two went against the party and took their seats.

A group of exiled opposition figures -- including defectors from Nkurunziza's party and leaders of a failed coup -- met in Ethiopian capital Addis Ababa on Thursday to set up an alternative government to defy the president.

Three former presidents, the exiled Burundi speaker of parliament and second deputy president were among more than 50 participants at the talks.

Diplomats say although there are some significant figures in this council, it is difficult to gauge how much of an influence it will have on the politics inside Burundi.